All cells after denoising

Major cell types

Only major cell types

## [1] "endothelial" "epithelial"  "immune"      "mesenchymal"

Major cell types and immune subtypes and T cells as a group

## [1] "Endothelial"  "Epithelial"   "Mesenchymal"  "Myeloid"      "NK_cells"    
## [6] "Other_immune" "T_cells"

Subtypes

All subtypes

##  [1] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
##  [5] "Tc_cells"      "Th_cells"      "Epithelial_1"  "Epithelial_10"
##  [9] "Epithelial_2"  "Epithelial_3"  "Epithelial_4"  "Epithelial_5" 
## [13] "Epithelial_6"  "Epithelial_7"  "Epithelial_8"  "Epithelial_9" 
## [17] "endothelial"   "mesenchymal"

Subtypes (T cells as one group)

##  [1] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
##  [5] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [9] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
## [13] "Epithelial_8"  "Epithelial_9"  "endothelial"   "mesenchymal"

Only Immune

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"

Only Epithelial

All epithelial subtypes

##  [1] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [5] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
##  [9] "Epithelial_8"  "Epithelial_9"

Stromal cells only

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"     "endothelial"  "mesenchymal"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "endothelial" 
## [6] "mesenchymal"

Exploring Rh negative only

Major cell types

Only major cell types

## [1] "endothelial" "epithelial"  "immune"      "mesenchymal"

Major cell types and immune subtypes and T cells as a group

## [1] "Endothelial"  "Epithelial"   "Mesenchymal"  "Myeloid"      "NK_cells"    
## [6] "Other_immune" "T_cells"

Subtypes

All subtypes

##  [1] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
##  [5] "Tc_cells"      "Th_cells"      "Epithelial_1"  "Epithelial_10"
##  [9] "Epithelial_2"  "Epithelial_3"  "Epithelial_4"  "Epithelial_5" 
## [13] "Epithelial_6"  "Epithelial_7"  "Epithelial_8"  "Epithelial_9" 
## [17] "endothelial"   "mesenchymal"

Subtypes (T cells as one group)

##  [1] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
##  [5] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [9] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
## [13] "Epithelial_8"  "Epithelial_9"  "endothelial"   "mesenchymal"

Only Immune

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"

Only Epithelial

All epithelial subtypes

##  [1] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [5] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
##  [9] "Epithelial_8"  "Epithelial_9"

Stromal cells only

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"     "endothelial"  "mesenchymal"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "endothelial" 
## [6] "mesenchymal"

Exploring Rh positive only

Major cell types

Only major cell types

## [1] "endothelial" "epithelial"  "immune"      "mesenchymal"

Major cell types and immune subtypes and T cells as a group

## [1] "Endothelial"  "Epithelial"   "Mesenchymal"  "Myeloid"      "NK_cells"    
## [6] "Other_immune" "T_cells"

Subtypes

All subtypes

##  [1] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
##  [5] "Tc_cells"      "Th_cells"      "Epithelial_1"  "Epithelial_10"
##  [9] "Epithelial_2"  "Epithelial_3"  "Epithelial_4"  "Epithelial_5" 
## [13] "Epithelial_6"  "Epithelial_7"  "Epithelial_8"  "Epithelial_9" 
## [17] "endothelial"   "mesenchymal"

Subtypes (T cells as one group)

##  [1] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
##  [5] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [9] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
## [13] "Epithelial_8"  "Epithelial_9"  "endothelial"   "mesenchymal"

Only Immune

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"

Only Epithelial

All epithelial subtypes

##  [1] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [5] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
##  [9] "Epithelial_8"  "Epithelial_9"

Stromal cells only

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"     "endothelial"  "mesenchymal"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "endothelial" 
## [6] "mesenchymal"

Cell types afected by removal of Rh+

## Total number of cells:  1721027
## Rh Negative number of cells:  111593
## Rh Positive number of cells:  1609434
## % of cells presumably lost in previous analysis:  93.51591 %

Total cell types percentages:

## 
## endothelial  epithelial      immune mesenchymal 
##    1.710607   47.305068   29.614004   21.370321
## 
##       Myeloid      NK_cells  Other_immune       T_cells      Tc_cells 
##      4.414399      1.943258     14.041209      6.705241      1.100971 
##      Th_cells  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##      1.408926      9.235706      2.483750      2.696878      6.562709 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##      1.325023      6.058185      7.575302      4.071058      6.303271 
##  Epithelial_9   endothelial   mesenchymal 
##      0.993186      1.710607     21.370321
## 
##       Myeloid      NK_cells  Other_immune       T_cells  Epithelial_1 
##      4.414399      1.943258     14.041209      9.215137      9.235706 
## Epithelial_10  Epithelial_2  Epithelial_3  Epithelial_4  Epithelial_5 
##      2.483750      2.696878      6.562709      1.325023      6.058185 
##  Epithelial_6  Epithelial_7  Epithelial_8  Epithelial_9   endothelial 
##      7.575302      4.071058      6.303271      0.993186      1.710607 
##   mesenchymal 
##     21.370321
## 
##  Endothelial   Epithelial  Mesenchymal      Myeloid     NK_cells Other_immune 
##     1.710607    47.305068    21.370321     4.414399     1.943258    14.041209 
##      T_cells 
##     9.215137

Rh negative cell types percentages:

## 
## endothelial  epithelial      immune mesenchymal 
##    1.536835   24.675383   48.145493   25.642289
## 
##       Myeloid      NK_cells  Other_immune       T_cells      Tc_cells 
##    13.2526234     1.6846935     5.9708046     3.2591650    10.9057020 
##      Th_cells  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##    13.0725045     0.3450037     0.6891113     0.8898408     1.8881113 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##     0.7491509     3.4132965     0.1155986     5.1983547     3.5073885 
##  Epithelial_9   endothelial   mesenchymal 
##     7.8795265     1.5368347    25.6422894
## 
##       Myeloid      NK_cells  Other_immune       T_cells  Epithelial_1 
##    13.2526234     1.6846935     5.9708046    27.2373715     0.3450037 
## Epithelial_10  Epithelial_2  Epithelial_3  Epithelial_4  Epithelial_5 
##     0.6891113     0.8898408     1.8881113     0.7491509     3.4132965 
##  Epithelial_6  Epithelial_7  Epithelial_8  Epithelial_9   endothelial 
##     0.1155986     5.1983547     3.5073885     7.8795265     1.5368347 
##   mesenchymal 
##    25.6422894
## 
##  Endothelial   Epithelial  Mesenchymal      Myeloid     NK_cells Other_immune 
##     1.536835    24.675383    25.642289    13.252623     1.684693     5.970805 
##      T_cells 
##    27.237372

Rh positive cell types percentages:

## 
## endothelial  epithelial      immune mesenchymal 
##    1.722655   48.874138   28.329090   21.074117
## 
##       Myeloid      NK_cells  Other_immune       T_cells      Tc_cells 
##     3.8015849     1.9611864    14.6007851     6.9441804     0.4211418 
##      Th_cells  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##     0.6002110     9.8521592     2.6081840     2.8221723     6.8868310 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##     1.3649519     6.2415731     8.0925344     3.9928944     6.4971288 
##  Epithelial_9   endothelial   mesenchymal 
##     0.5157092     1.7226553    21.0741167
## 
##       Myeloid      NK_cells  Other_immune       T_cells  Epithelial_1 
##     3.8015849     1.9611864    14.6007851     7.9655332     9.8521592 
## Epithelial_10  Epithelial_2  Epithelial_3  Epithelial_4  Epithelial_5 
##     2.6081840     2.8221723     6.8868310     1.3649519     6.2415731 
##  Epithelial_6  Epithelial_7  Epithelial_8  Epithelial_9   endothelial 
##     8.0925344     3.9928944     6.4971288     0.5157092     1.7226553 
##   mesenchymal 
##    21.0741167
## 
##  Endothelial   Epithelial  Mesenchymal      Myeloid     NK_cells Other_immune 
##     1.722655    48.874138    21.074117     3.801585     1.961186    14.600785 
##      T_cells 
##     7.965533

Heatmaps

All cells

Rh negative

Rh positive

Other Comparisons

## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables